Complete nucleotide sequence of a cryptic plasmid, pbaw301, from the ruminai anaerobe Ruminococcus flavefaciens R13e2

Abstract The complete nucleotide sequence of a cryptic plasmid designated pBAW301, from the Gram-positive ruminai bacterium Ruminococcus flavefaciens R13e2, has been determined. This plasmid is 1768 bp in size and has an overall G+C content of 43.5%. Computer analysis of the sequence data revealed an open reading frame, ORF1 (256 amino acids), which is similar to the Rep protein of the Bacillus borstelensis plasmid pHT926. ORF1 is preceded by Shine-Dalgarno and Escherichia coli —10 and —35 like sequences. Nine smaller open reading frames showed no significant homologies to known protein sequences. Analysis of replication intermediates and the nucleotide sequence indicate that the plasmid does not replicate by a rolling-circle mode of replication similar to other plasmids from Gram-positive bacteria. Moreover, sequences typical of theta replication origins were not found in the nucleotide sequence of pBAW301. These data suggest that this plasmid either replicates by an as yet undescribed mechanism, or represents a new class of theta replicating plasmids.     

Selection of the conodont Idiognathodus simulator (Ellison) as the event marker for the base of the global Gzhelian Stage (Upper Pennsylvanian, Carboniferous)

Studies carried out for more than 10 years by the Task Group to establish GSSPs at the base of the Moscovian–Kasimovian and Kasimovian–Gzhelian boundaries have resulted in the proposal that the level at which the conodont species Idiognathodus simulator (Ellison, 1941) first appears be selected to mark the base of the Gzhelian Stage. This expands this eastern European chronostratigraphic unit to a global scale.I. simulator (sensu Barrick et al., 2008) has been identified so far in Midcontinent and eastern North America, the Moscow and Donets basins and southern Urals of eastern Europe, and in south-central China. Correlation of this level based on this species and other conodont species can be reinforced in some areas by ammonoid and fusulinid data.     

Post‐glacial history and introgression in Abies (Pinaceae) species of the Russian Far East inferred from both nuclear and cytoplasmic markers

Aim The main aim of the present study is to infer the post‐glacial history of Abies species from north‐east Asia and to test the hypotheses that coastal Abies populations suffered less from climatic fluctuations during Pleistocene glacial periods than their more continental counterparts, and that Sakhalin was a major area of introgression. Location Natural ranges of the fir species Abies nephrolepis, Abies sachalinensis and Abies holophylla in the Russian Far East, and of Abies gracilis, which is endemic to the Kamchatka Peninsula. Methods Nineteen populations were sampled for allozyme analysis. Seventeen of these populations were also screened for variation at two paternally inherited chloroplast DNA microsatellite loci (cpSSR) and variation at one maternally inherited mitochondrial marker (nad4‐3/4). Finally a subset of 11 populations was analysed with amplified fragment length polymorphism (AFLP). Comparisons were made with already available Abies sibirica data. For all sets of markers, we estimated genetic diversity and differentiation using an analysis of molecular variance (AMOVA). Population clustering was assessed with a Bayesian approach implemented in structure v.2.3. Results Among the three major species, A. sibirica, A. nephrolepis and A. sachalinensis, A. sachalinensis demonstrated the highest cytoplasmic and nuclear diversity and the most continental species, A. sibirica, the lowest. Both nuclear and mitochondrial DNA markers revealed the presence of a transitional zone on Sakhalin Island between A. nephrolepis and A. sachalinensis of south Sakhalin. The structure analysis delivered very clear results confirming the admixed origin of A. sachalinensis, with a genetic contribution from A. nephrolepis. No variation in cytoplasmic markers was found in A. gracilis, suggesting the occurrence of a recent bottleneck. Main conclusions There is a clear reduction of genetic diversity in Abies species from the Pacific coast into the continent. The higher diversity in A. sachalinensis could have two causes: a larger effective population size in the islands due to relatively stable climatic conditions and consequently less pronounced demographic fluctuations in population size and/or hybridization with continental and Japanese populations. Sakhalin Island is a major transitional zone for conifer species. Finally, the fir from Kamchatka, A. gracilis, should be regarded as a separate species closely related to the A. nephrolepis–A. sachalinensis complex.     

Construction of an l-phenylalanine-producing tyrosine-prototrophic Escherichia coli strain using tyrA ssrA-like tagged alleles

To construct a Phe-producing Tyr⁺ Escherichia coli strain, TyrA (chorismate mutase/prephenate dehydrogenase) activity was varied by engineering a proteolytically unstable protein. The tyrA in the E. coli BW25113 was altered to include ssrA-like tags. The tagged tyrA genes, which ensured different growth rates in M9 medium, were introduced into a Phe-producing strain to replace ΔtyrA. Strains with unstable TyrA-(A)ANDENYALAA proteins had a lower biomass yield and a higher Phe accumulation than strains generating the more stable TyrA-(A)ANDENYALDD. The Tyr/Phe ratio produced by the TyrA-tag strains was 10-fold less than that produced by the TyrA^wt strain.     

A small RNA controls a protein regulator involved in antibiotic resistance in Staphylococcus aureus

The emergence of Staphylococcus aureus strains that are resistant to glycopeptides has led to alarming scenarios where serious staphylococcal infections cannot be treated. The bacterium expresses many small regulatory RNAs (sRNAs) that have unknown biological functions for the most part. Here we show that an S. aureus sRNA, SprX (alias RsaOR), shapes bacterial resistance to glycopeptides, the invaluable treatments for Methicillin-resistant staphylococcal infections. Modifying SprX expression levels influences Vancomycin and Teicoplanin glycopeptide resistance. Comparative proteomic studies have identified that SprX specifically downregulates stage V sporulation protein G, SpoVG. SpoVG is produced from the yabJ-spoVG operon and contributes to S. aureus glycopeptide resistance. SprX negatively regulates SpoVG expression by direct antisense pairings at the internal translation initiation signals of the second operon gene, without modifying bicistronic mRNA expression levels or affecting YabJ translation. The SprX and yabJ-spoVG mRNA domains involved in the interaction have been identified, highlighting the importance of a CU-rich loop of SprX in the control of SpoVG expression. We have shown that SpoVG might not be the unique SprX target involved in the glycopeptide resistance and demonstrated that the regulation of glycopeptide sensitivity involves the CU-rich domain of SprX. Here we report the case of a sRNA influencing antibiotic resistance of a major human pathogen.     

Development of seawater adaptation in pink salmon,Oncorhynchus gorbuscha,during downstream migration: relationships to temperature and residual yolk

Synopsis Seawater adaptability of wild pink salmon, Oncorhynchus gorbuscha, alevins was investigated using 96 h LC50 test, muscle sodium level and weight loss tests. Five temperature (2, 6, 9, 13 and 16°C) and two yolk groups were analysed during the beginning, the middle and the end of downstream migration. Both temperature and amount of residual yolk affected seawater adaptability. The computation of muscle sodium levels and weight loss after a short term (3–12 h) seawater challenge test may be a convenient method to estimate the seawater adaptability of fish too small to allow analysis of blood sodium concentration.